Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: AWUE01014905.1 Corchorus olitorius cultivar O-4 contig14938, whole genome shotgun sequence

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 35249
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.30


Found at i:4610 original size:15 final size:13

Alignment explanation


    Indices: 4579--4618  Score: 53
    Period size: 15  Copynumber: 2.8  Consensus size: 13

       4569 AAAACAGGGG

                         
       4579 ATTAAATAAAACA
          1 ATTAAATAAAACA

                           
       4592 ATTAAATCAAAAGCA
          1 ATTAAAT-AAAA-CA

                        
       4607 ATTAAACTAAAA
          1 ATTAAA-TAAAA

       4619 AATAAAGCAA


Statistics
Matches: 24,  Mismatches: 0, Indels: 4
        0.86            0.00        0.14

Matches are distributed among these distances:
  13    7  0.29
  14    4  0.17
  15   12  0.50
  16    1  0.04

ACGTcount: A:0.65, C:0.10, G:0.03, T:0.23


Consensus pattern (13 bp):   
ATTAAATAAAACA

Found at i:7725 original size:16 final size:16

Alignment explanation


    Indices: 7704--7737  Score: 50
    Period size: 16  Copynumber: 2.1  Consensus size: 16

       7694 AGGAATAGGC

                            
       7704 AATCAATAAAAGCAAT
          1 AATCAATAAAAGCAAT

                   *    *   
       7720 AATCAATCAAAGGAAT
          1 AATCAATAAAAGCAAT

              
       7736 AA
          1 AA

       7738 AGGCAAAGAA


Statistics
Matches: 16,  Mismatches: 2, Indels: 0
        0.89            0.11        0.00

Matches are distributed among these distances:
  16   16  1.00

ACGTcount: A:0.62, C:0.12, G:0.09, T:0.18


Consensus pattern (16 bp):   
AATCAATAAAAGCAAT

Found at i:18455 original size:30 final size:30

Alignment explanation


    Indices: 18400--18457  Score: 107
    Period size: 30  Copynumber: 1.9  Consensus size: 30

      18390 CATTAGCAGC

                                          
      18400 CGTTCTAAATCAACGATTATCAAGATCAGT
          1 CGTTCTAAATCAACGATTATCAAGATCAGT

                                *       
      18430 CGTTCTAAATCAACGATTATTAAGATCA
          1 CGTTCTAAATCAACGATTATCAAGATCA

      18458 TAAAATAAAA


Statistics
Matches: 27,  Mismatches: 1, Indels: 0
        0.96            0.04        0.00

Matches are distributed among these distances:
  30   27  1.00

ACGTcount: A:0.38, C:0.19, G:0.12, T:0.31


Consensus pattern (30 bp):   
CGTTCTAAATCAACGATTATCAAGATCAGT

Found at i:22082 original size:35 final size:38

Alignment explanation


    Indices: 22043--22122  Score: 103
    Period size: 37  Copynumber: 2.2  Consensus size: 38

      22033 TTTCTTAATT

                                                  
      22043 TTAATTGTTTTC-TCAA-TTTATTCATTGCTTTC-TAC
          1 TTAATTGTTTTCTTCAATTTTATTCATTGCTTTCTTAC

                          *      *  *            *
      22078 TTAATTGTTTTCTTTAATTTTCTTGATTGCTTTCTTAG
          1 TTAATTGTTTTCTTCAATTTTATTCATTGCTTTCTTAC

                   
      22116 TTAATTG
          1 TTAATTG

      22123 CTTTGATTTT


Statistics
Matches: 38,  Mismatches: 4, Indels: 3
        0.84            0.09        0.07

Matches are distributed among these distances:
  35   12  0.32
  36    3  0.08
  37   14  0.37
  38    9  0.24

ACGTcount: A:0.19, C:0.12, G:0.09, T:0.60


Consensus pattern (38 bp):   
TTAATTGTTTTCTTCAATTTTATTCATTGCTTTCTTAC

Found at i:35157 original size:42 final size:41

Alignment explanation


    Indices: 35085--35168  Score: 109
    Period size: 42  Copynumber: 2.0  Consensus size: 41

      35075 AAAATTATTA

                                     *                
      35085 AAATAAAATAAAAAAAGTAATAGATGAATAAATAA-ATAAAT
          1 AAATAAAATAAAAAAAGTAATAGATAAATAAA-AAGATAAAT

                         *                             
      35126 AAATAAAATAAGTGAAAA-TAATAGATAAATAAAAAGATAAAT
          1 AAATAAAATAA--AAAAAGTAATAGATAAATAAAAAGATAAAT

             
      35168 A
          1 A

      35169 GGTATATAGA


Statistics
Matches: 38,  Mismatches: 2, Indels: 5
        0.84            0.04        0.11

Matches are distributed among these distances:
  41   13  0.34
  42   21  0.55
  43    4  0.11

ACGTcount: A:0.70, C:0.00, G:0.08, T:0.21


Consensus pattern (41 bp):   
AAATAAAATAAAAAAAGTAATAGATAAATAAAAAGATAAAT

Found at i:35193 original size:16 final size:16

Alignment explanation


    Indices: 35103--35193  Score: 53
    Period size: 16  Copynumber: 5.8  Consensus size: 16

      35093 TAAAAAAAGT

                   *    *   
      35103 AATAGATGAATAAATA
          1 AATAGATAAATAGATA

                *        *   
      35119 AATAAATAAATAAAATA
          1 AATAGATAAAT-AGATA

             *              
      35136 AGT-GA-AAATA-ATA
          1 AATAGATAAATAGATA

            *   *     *     
      35149 GATAAATAAAAAGATA
          1 AATAGATAAATAGATA

                 *  *       
      35165 AATAGGTATATAGATA
          1 AATAGATAAATAGATA

             *           
      35181 ATTAGATAAATAG
          1 AATAGATAAATAG

      35194 GTAGGTAAAA


Statistics
Matches: 55,  Mismatches: 16, Indels: 8
        0.70            0.20        0.10

Matches are distributed among these distances:
  13    4  0.07
  14    2  0.04
  15    8  0.15
  16   34  0.62
  17    7  0.13

ACGTcount: A:0.63, C:0.00, G:0.12, T:0.25


Consensus pattern (16 bp):   
AATAGATAAATAGATA
Done.